If you can train your dog to be comfortable in the woods and not feel like it has to protect you from every little sound and strange person that comes along and not to chase wildlife (more then a few dogs have been lost after they run after something and can't find their way back), it shouldn't be too much of an issue.

Speaking of dogs which run off and can't find their way back, it's probably a good idea to train your dog to return to the sound of a whistle, which will carry much farther then you shouting "get back here fluffy".

Weekend / day hiker dogs are usually the worst offenders as they are often not trained very well. Their not out there long enough or often enough to become comfortable with being in the woods or encountering non-family members. A lot of it depends on the temperament of the breed - and the owner.

OTOH, after a week or two a thru hiker dog is so tired at the end of the day all it wants to do is go to sleep. That first week or two while it gets used to the idea if not conditioned first can be a problem though.